Starting phenix.real_space_refine on Sun Feb 8 01:08:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oqo_70768/02_2026/9oqo_70768_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oqo_70768/02_2026/9oqo_70768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oqo_70768/02_2026/9oqo_70768_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oqo_70768/02_2026/9oqo_70768_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oqo_70768/02_2026/9oqo_70768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oqo_70768/02_2026/9oqo_70768.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 77 5.16 5 C 12754 2.51 5 N 2898 2.21 5 O 3234 1.98 5 H 17927 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36897 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 5.87, per 1000 atoms: 0.16 Number of scatterers: 36897 At special positions: 0 Unit cell: (109.65, 110.5, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 7 15.00 O 3234 8.00 N 2898 7.00 C 12754 6.00 H 17927 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 504 " - " ASN A 255 " " NAG B 504 " - " ASN B 255 " " NAG C 504 " - " ASN C 255 " " NAG D 504 " - " ASN D 255 " " NAG E 504 " - " ASN E 255 " " NAG F 504 " - " ASN F 255 " " NAG G 504 " - " ASN G 255 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 68.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.567A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 100 through 131 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 Processing helix chain 'A' and resid 194 through 206 removed outlier: 3.898A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.715A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.543A pdb=" N VAL A 308 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.843A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.697A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.567A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 100 through 131 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.899A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.716A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.543A pdb=" N VAL B 308 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.843A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 356 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.698A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.567A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 100 through 131 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 Processing helix chain 'C' and resid 194 through 206 removed outlier: 3.898A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.715A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.542A pdb=" N VAL C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.843A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 356 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.697A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.567A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 100 through 131 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.899A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.715A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 312 removed outlier: 3.543A pdb=" N VAL D 308 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.843A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 356 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.697A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.567A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 100 through 131 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 Processing helix chain 'E' and resid 194 through 206 removed outlier: 3.899A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.715A pdb=" N ARG E 300 " --> pdb=" O PHE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 312 removed outlier: 3.543A pdb=" N VAL E 308 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.844A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 356 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.697A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.567A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 100 through 131 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.899A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.716A pdb=" N ARG F 300 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 312 removed outlier: 3.543A pdb=" N VAL F 308 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.844A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 356 Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.698A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.567A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 100 through 131 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.899A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.715A pdb=" N ARG G 300 " --> pdb=" O PHE G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 312 removed outlier: 3.543A pdb=" N VAL G 308 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.843A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 356 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.697A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.639A pdb=" N VAL A 245 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.638A pdb=" N VAL B 245 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.639A pdb=" N VAL C 245 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.638A pdb=" N VAL D 245 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.638A pdb=" N VAL E 245 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.639A pdb=" N VAL F 245 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.638A pdb=" N VAL G 245 " --> pdb=" O GLN G 95 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17892 1.03 - 1.23: 56 1.23 - 1.42: 7749 1.42 - 1.62: 11550 1.62 - 1.81: 105 Bond restraints: 37352 Sorted by residual: bond pdb=" C GLU A 19 " pdb=" N PRO A 20 " ideal model delta sigma weight residual 1.330 1.339 -0.008 1.19e-02 7.06e+03 4.88e-01 bond pdb=" C PHE C 296 " pdb=" N VAL C 297 " ideal model delta sigma weight residual 1.329 1.337 -0.008 1.13e-02 7.83e+03 4.46e-01 bond pdb=" C GLU E 19 " pdb=" N PRO E 20 " ideal model delta sigma weight residual 1.330 1.338 -0.008 1.19e-02 7.06e+03 4.44e-01 bond pdb=" C PHE G 296 " pdb=" N VAL G 297 " ideal model delta sigma weight residual 1.329 1.337 -0.008 1.13e-02 7.83e+03 4.42e-01 bond pdb=" C GLU C 19 " pdb=" N PRO C 20 " ideal model delta sigma weight residual 1.330 1.338 -0.008 1.19e-02 7.06e+03 4.39e-01 ... (remaining 37347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 63000 1.08 - 2.17: 4115 2.17 - 3.25: 148 3.25 - 4.33: 63 4.33 - 5.41: 21 Bond angle restraints: 67347 Sorted by residual: angle pdb=" N LEU C 30 " pdb=" CA LEU C 30 " pdb=" CB LEU C 30 " ideal model delta sigma weight residual 113.65 110.86 2.79 1.47e+00 4.63e-01 3.60e+00 angle pdb=" N LEU F 30 " pdb=" CA LEU F 30 " pdb=" CB LEU F 30 " ideal model delta sigma weight residual 113.65 110.86 2.79 1.47e+00 4.63e-01 3.59e+00 angle pdb=" N LEU G 30 " pdb=" CA LEU G 30 " pdb=" CB LEU G 30 " ideal model delta sigma weight residual 113.65 110.88 2.77 1.47e+00 4.63e-01 3.54e+00 angle pdb=" N LEU A 30 " pdb=" CA LEU A 30 " pdb=" CB LEU A 30 " ideal model delta sigma weight residual 113.65 110.92 2.73 1.47e+00 4.63e-01 3.46e+00 angle pdb=" N LEU B 30 " pdb=" CA LEU B 30 " pdb=" CB LEU B 30 " ideal model delta sigma weight residual 113.65 110.93 2.72 1.47e+00 4.63e-01 3.44e+00 ... (remaining 67342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 17506 16.97 - 33.93: 918 33.93 - 50.90: 224 50.90 - 67.87: 91 67.87 - 84.83: 14 Dihedral angle restraints: 18753 sinusoidal: 10192 harmonic: 8561 Sorted by residual: dihedral pdb=" CA GLU E 9 " pdb=" C GLU E 9 " pdb=" N TYR E 10 " pdb=" CA TYR E 10 " ideal model delta harmonic sigma weight residual 180.00 -164.44 -15.56 0 5.00e+00 4.00e-02 9.68e+00 dihedral pdb=" CA GLU B 9 " pdb=" C GLU B 9 " pdb=" N TYR B 10 " pdb=" CA TYR B 10 " ideal model delta harmonic sigma weight residual -180.00 -164.45 -15.55 0 5.00e+00 4.00e-02 9.67e+00 dihedral pdb=" CA GLU A 9 " pdb=" C GLU A 9 " pdb=" N TYR A 10 " pdb=" CA TYR A 10 " ideal model delta harmonic sigma weight residual -180.00 -164.45 -15.55 0 5.00e+00 4.00e-02 9.67e+00 ... (remaining 18750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2578 0.040 - 0.080: 495 0.080 - 0.120: 146 0.120 - 0.160: 8 0.160 - 0.200: 7 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG D 504 " pdb=" ND2 ASN D 255 " pdb=" C2 NAG D 504 " pdb=" O5 NAG D 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" C1 NAG G 504 " pdb=" ND2 ASN G 255 " pdb=" C2 NAG G 504 " pdb=" O5 NAG G 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" C1 NAG E 504 " pdb=" ND2 ASN E 255 " pdb=" C2 NAG E 504 " pdb=" O5 NAG E 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 3231 not shown) Planarity restraints: 5432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 122 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO G 123 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO G 123 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 123 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 122 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO E 123 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 122 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO D 123 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.018 5.00e-02 4.00e+02 ... (remaining 5429 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 15288 2.39 - 2.94: 84603 2.94 - 3.49: 100144 3.49 - 4.05: 128978 4.05 - 4.60: 198744 Nonbonded interactions: 527757 Sorted by model distance: nonbonded pdb="HE22 GLN E 90 " pdb=" HZ1 LYS F 266 " model vdw 1.833 2.100 nonbonded pdb=" HZ1 LYS A 266 " pdb="HE22 GLN G 90 " model vdw 1.838 2.100 nonbonded pdb="HE22 GLN A 90 " pdb=" HZ1 LYS B 266 " model vdw 1.839 2.100 nonbonded pdb="HE22 GLN D 90 " pdb=" HZ1 LYS E 266 " model vdw 1.848 2.100 nonbonded pdb="HE22 GLN C 90 " pdb=" HZ1 LYS D 266 " model vdw 1.853 2.100 ... (remaining 527752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.250 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.720 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19446 Z= 0.117 Angle : 0.511 5.414 26572 Z= 0.267 Chirality : 0.036 0.200 3234 Planarity : 0.003 0.032 3136 Dihedral : 11.813 84.833 7679 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.38 % Allowed : 4.18 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2380 helix: 2.42 (0.14), residues: 1603 sheet: None (None), residues: 0 loop : -1.28 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 128 TYR 0.008 0.001 TYR C 83 PHE 0.007 0.001 PHE B 244 TRP 0.009 0.002 TRP D 104 HIS 0.002 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00265 (19425) covalent geometry : angle 0.50820 (26523) SS BOND : bond 0.00265 ( 14) SS BOND : angle 0.98114 ( 28) hydrogen bonds : bond 0.08871 ( 1205) hydrogen bonds : angle 4.13897 ( 3531) link_NAG-ASN : bond 0.00451 ( 7) link_NAG-ASN : angle 1.64653 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 235 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 230 TYR cc_start: 0.7475 (t80) cc_final: 0.7165 (t80) outliers start: 7 outliers final: 7 residues processed: 235 average time/residue: 0.3592 time to fit residues: 126.1203 Evaluate side-chains 122 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain G residue 74 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 235 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN D 280 ASN E 280 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.096052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.075388 restraints weight = 185935.940| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.83 r_work: 0.3192 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19446 Z= 0.181 Angle : 0.529 5.772 26572 Z= 0.274 Chirality : 0.036 0.186 3234 Planarity : 0.003 0.030 3136 Dihedral : 6.575 59.923 3871 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.54 % Allowed : 10.54 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.18), residues: 2380 helix: 2.49 (0.13), residues: 1603 sheet: None (None), residues: 0 loop : -1.35 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 29 TYR 0.010 0.001 TYR F 213 PHE 0.008 0.001 PHE B 67 TRP 0.004 0.001 TRP D 104 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00389 (19425) covalent geometry : angle 0.52716 (26523) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.90608 ( 28) hydrogen bonds : bond 0.03352 ( 1205) hydrogen bonds : angle 4.00064 ( 3531) link_NAG-ASN : bond 0.00216 ( 7) link_NAG-ASN : angle 1.27265 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8904 (m-30) cc_final: 0.8701 (m-30) REVERT: C 81 ASP cc_start: 0.8868 (m-30) cc_final: 0.8654 (m-30) REVERT: G 81 ASP cc_start: 0.8935 (m-30) cc_final: 0.8724 (m-30) outliers start: 10 outliers final: 9 residues processed: 144 average time/residue: 0.2979 time to fit residues: 69.4132 Evaluate side-chains 126 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 74 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 151 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.092621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071886 restraints weight = 188341.688| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.69 r_work: 0.3129 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19446 Z= 0.293 Angle : 0.606 5.575 26572 Z= 0.322 Chirality : 0.039 0.197 3234 Planarity : 0.004 0.030 3136 Dihedral : 7.133 66.031 3871 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.41 % Allowed : 12.28 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.18), residues: 2380 helix: 2.23 (0.13), residues: 1603 sheet: None (None), residues: 0 loop : -1.59 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 29 TYR 0.012 0.002 TYR F 230 PHE 0.016 0.001 PHE B 67 TRP 0.004 0.001 TRP E 74 HIS 0.004 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00609 (19425) covalent geometry : angle 0.60523 (26523) SS BOND : bond 0.00383 ( 14) SS BOND : angle 1.11664 ( 28) hydrogen bonds : bond 0.03809 ( 1205) hydrogen bonds : angle 4.36512 ( 3531) link_NAG-ASN : bond 0.00019 ( 7) link_NAG-ASN : angle 0.66777 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8885 (tp40) cc_final: 0.8651 (tp40) outliers start: 26 outliers final: 25 residues processed: 144 average time/residue: 0.2932 time to fit residues: 68.1911 Evaluate side-chains 145 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 169 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 194 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.094698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073773 restraints weight = 185291.127| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.76 r_work: 0.3138 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19446 Z= 0.144 Angle : 0.506 5.538 26572 Z= 0.260 Chirality : 0.036 0.180 3234 Planarity : 0.003 0.033 3136 Dihedral : 6.717 65.206 3871 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.36 % Allowed : 12.66 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.19), residues: 2380 helix: 2.50 (0.13), residues: 1603 sheet: None (None), residues: 0 loop : -1.50 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 29 TYR 0.012 0.001 TYR A 230 PHE 0.008 0.001 PHE B 67 TRP 0.005 0.001 TRP D 104 HIS 0.002 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00312 (19425) covalent geometry : angle 0.50547 (26523) SS BOND : bond 0.00109 ( 14) SS BOND : angle 0.63694 ( 28) hydrogen bonds : bond 0.03270 ( 1205) hydrogen bonds : angle 4.05694 ( 3531) link_NAG-ASN : bond 0.00208 ( 7) link_NAG-ASN : angle 1.05950 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 138 average time/residue: 0.2825 time to fit residues: 64.6330 Evaluate side-chains 134 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 193 optimal weight: 0.0270 chunk 51 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 202 optimal weight: 0.0970 chunk 228 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.094332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073513 restraints weight = 185705.392| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.75 r_work: 0.3136 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19446 Z= 0.151 Angle : 0.503 5.452 26572 Z= 0.259 Chirality : 0.036 0.173 3234 Planarity : 0.003 0.033 3136 Dihedral : 6.563 61.078 3871 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.90 % Allowed : 11.84 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.19), residues: 2380 helix: 2.53 (0.13), residues: 1603 sheet: None (None), residues: 0 loop : -1.48 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 29 TYR 0.012 0.001 TYR A 230 PHE 0.008 0.001 PHE G 244 TRP 0.005 0.001 TRP D 104 HIS 0.001 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00326 (19425) covalent geometry : angle 0.50237 (26523) SS BOND : bond 0.00149 ( 14) SS BOND : angle 0.66113 ( 28) hydrogen bonds : bond 0.03176 ( 1205) hydrogen bonds : angle 4.02885 ( 3531) link_NAG-ASN : bond 0.00203 ( 7) link_NAG-ASN : angle 1.00212 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLN cc_start: 0.8761 (mp10) cc_final: 0.8519 (mp10) REVERT: F 243 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8292 (mt-10) outliers start: 35 outliers final: 27 residues processed: 139 average time/residue: 0.2705 time to fit residues: 63.1293 Evaluate side-chains 137 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.093053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071931 restraints weight = 186921.958| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.72 r_work: 0.3117 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 19446 Z= 0.269 Angle : 0.577 5.982 26572 Z= 0.304 Chirality : 0.038 0.181 3234 Planarity : 0.004 0.033 3136 Dihedral : 7.122 63.843 3871 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.23 % Allowed : 12.49 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.18), residues: 2380 helix: 2.27 (0.13), residues: 1603 sheet: None (None), residues: 0 loop : -1.66 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.016 0.001 TYR G 230 PHE 0.015 0.001 PHE F 67 TRP 0.004 0.001 TRP D 104 HIS 0.004 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00562 (19425) covalent geometry : angle 0.57661 (26523) SS BOND : bond 0.00408 ( 14) SS BOND : angle 1.14242 ( 28) hydrogen bonds : bond 0.03658 ( 1205) hydrogen bonds : angle 4.29260 ( 3531) link_NAG-ASN : bond 0.00022 ( 7) link_NAG-ASN : angle 0.53897 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLN cc_start: 0.8870 (mp10) cc_final: 0.8651 (mp10) REVERT: F 243 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8237 (mp0) outliers start: 41 outliers final: 32 residues processed: 144 average time/residue: 0.2630 time to fit residues: 64.6898 Evaluate side-chains 148 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 280 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 189 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 152 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 169 optimal weight: 0.0020 chunk 2 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.094751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073738 restraints weight = 184598.869| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.76 r_work: 0.3131 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19446 Z= 0.138 Angle : 0.513 6.561 26572 Z= 0.263 Chirality : 0.036 0.170 3234 Planarity : 0.003 0.035 3136 Dihedral : 6.836 63.504 3871 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.47 % Allowed : 12.55 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 2380 helix: 2.56 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -1.57 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 75 TYR 0.011 0.001 TYR G 230 PHE 0.013 0.001 PHE D 244 TRP 0.005 0.001 TRP D 104 HIS 0.001 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00302 (19425) covalent geometry : angle 0.51245 (26523) SS BOND : bond 0.00145 ( 14) SS BOND : angle 0.65430 ( 28) hydrogen bonds : bond 0.03286 ( 1205) hydrogen bonds : angle 4.00077 ( 3531) link_NAG-ASN : bond 0.00193 ( 7) link_NAG-ASN : angle 0.90633 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLN cc_start: 0.8859 (mp10) cc_final: 0.8645 (mp10) REVERT: F 243 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8192 (mp0) outliers start: 27 outliers final: 27 residues processed: 130 average time/residue: 0.2477 time to fit residues: 53.9714 Evaluate side-chains 136 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 276 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 147 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 235 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 280 ASN G 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.094913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073929 restraints weight = 184070.380| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.77 r_work: 0.3135 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19446 Z= 0.139 Angle : 0.508 6.510 26572 Z= 0.260 Chirality : 0.036 0.167 3234 Planarity : 0.003 0.034 3136 Dihedral : 6.686 61.297 3871 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.74 % Allowed : 12.60 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.19), residues: 2380 helix: 2.61 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 75 TYR 0.011 0.001 TYR G 230 PHE 0.007 0.001 PHE G 67 TRP 0.005 0.001 TRP D 104 HIS 0.001 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00304 (19425) covalent geometry : angle 0.50706 (26523) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.66683 ( 28) hydrogen bonds : bond 0.03207 ( 1205) hydrogen bonds : angle 3.93949 ( 3531) link_NAG-ASN : bond 0.00186 ( 7) link_NAG-ASN : angle 0.92905 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLN cc_start: 0.8873 (mp10) cc_final: 0.8646 (mp10) REVERT: F 243 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8192 (mp0) outliers start: 32 outliers final: 27 residues processed: 131 average time/residue: 0.2387 time to fit residues: 53.1647 Evaluate side-chains 135 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 177 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 219 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 148 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.093252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072314 restraints weight = 184741.431| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.71 r_work: 0.3108 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19446 Z= 0.221 Angle : 0.551 6.201 26572 Z= 0.288 Chirality : 0.036 0.163 3234 Planarity : 0.004 0.034 3136 Dihedral : 7.021 63.511 3871 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.79 % Allowed : 12.87 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2380 helix: 2.44 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -1.65 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 254 TYR 0.013 0.001 TYR G 230 PHE 0.011 0.001 PHE F 67 TRP 0.004 0.001 TRP E 104 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00465 (19425) covalent geometry : angle 0.54996 (26523) SS BOND : bond 0.00337 ( 14) SS BOND : angle 1.05392 ( 28) hydrogen bonds : bond 0.03496 ( 1205) hydrogen bonds : angle 4.11201 ( 3531) link_NAG-ASN : bond 0.00008 ( 7) link_NAG-ASN : angle 0.71542 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLN cc_start: 0.8970 (mp10) cc_final: 0.8743 (mp10) REVERT: D 57 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8811 (pm20) REVERT: F 243 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8180 (mp0) outliers start: 33 outliers final: 29 residues processed: 139 average time/residue: 0.2442 time to fit residues: 58.2895 Evaluate side-chains 144 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 188 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 208 optimal weight: 0.4980 chunk 36 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 42 optimal weight: 0.0870 chunk 168 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 280 ASN G 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.095612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.074868 restraints weight = 183194.388| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.78 r_work: 0.3160 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19446 Z= 0.097 Angle : 0.493 6.144 26572 Z= 0.249 Chirality : 0.035 0.156 3234 Planarity : 0.003 0.035 3136 Dihedral : 6.526 61.091 3871 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.52 % Allowed : 13.31 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 2380 helix: 2.69 (0.14), residues: 1596 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 217 TYR 0.010 0.001 TYR D 230 PHE 0.006 0.001 PHE A 79 TRP 0.007 0.001 TRP C 104 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00223 (19425) covalent geometry : angle 0.49224 (26523) SS BOND : bond 0.00087 ( 14) SS BOND : angle 0.61544 ( 28) hydrogen bonds : bond 0.03036 ( 1205) hydrogen bonds : angle 3.79356 ( 3531) link_NAG-ASN : bond 0.00284 ( 7) link_NAG-ASN : angle 1.20535 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLN cc_start: 0.8921 (mp10) cc_final: 0.8628 (mp10) REVERT: F 243 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8164 (mt-10) outliers start: 28 outliers final: 21 residues processed: 131 average time/residue: 0.2411 time to fit residues: 53.5516 Evaluate side-chains 129 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 280 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 234 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 280 ASN G 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.095433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.074495 restraints weight = 183566.984| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.78 r_work: 0.3148 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 19446 Z= 0.170 Angle : 0.676 59.200 26572 Z= 0.382 Chirality : 0.036 0.157 3234 Planarity : 0.003 0.035 3136 Dihedral : 6.520 61.207 3871 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.68 % Allowed : 13.42 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.19), residues: 2380 helix: 2.67 (0.14), residues: 1596 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 217 TYR 0.007 0.001 TYR G 10 PHE 0.006 0.001 PHE F 244 TRP 0.007 0.001 TRP C 104 HIS 0.001 0.000 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00363 (19425) covalent geometry : angle 0.67577 (26523) SS BOND : bond 0.00131 ( 14) SS BOND : angle 0.42218 ( 28) hydrogen bonds : bond 0.03076 ( 1205) hydrogen bonds : angle 3.85553 ( 3531) link_NAG-ASN : bond 0.00213 ( 7) link_NAG-ASN : angle 1.13337 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6886.14 seconds wall clock time: 118 minutes 12.59 seconds (7092.59 seconds total)